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Coupled models of genomic surveillance and evolving pandemics with applications for timely public health interventions

Espinoza, B and Adiga, A and Venkatramanan, S and Warren, AS and Chen, J and Lewis, BL and Vullikanti, A and Swarup, S and Moon, S and Barrett, CL and Athreya, S and Sundaresan, R and Chandru, V and Laxminarayan, R and Schaffer, B and Poor, HV and Levin, SA and Marathe, MV (2023) Coupled models of genomic surveillance and evolving pandemics with applications for timely public health interventions. In: Proceedings of the National Academy of Sciences of the United States of America, 120 (48).

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Official URL: https://doi.org/10.1073/pnas.2305227120


Disease surveillance systems provide early warnings of disease outbreaks before they become public health emergencies. However, pandemics containment would be challenging due to the complex immunity landscape created by multiple variants. Genomic surveillance is critical for detecting novel variants with diverse characteristics and importation/emergence times. Yet, a systematic study incorporating genomic monitoring, situation assessment, and intervention strategies is lacking in the literature. We formulate an integrated computational modeling framework to study a realistic course of action based on sequencing, analysis, and response. We study the effects of the second variant�s importation time, its infectiousness advantage and, its cross-infection on the novel variant�s detection time, and the resulting intervention scenarios to contain epidemics driven by two-variants dynamics. Our results illustrate the limitation in the intervention�s effectiveness due to the variants� competing dynamics and provide the following insights: i) There is a set of importation times that yields the worst detection time for the second variant, which depends on the first variant�s basic reproductive number; ii) When the second variant is imported relatively early with respect to the first variant, the cross-infection level does not impact the detection time of the second variant. We found that depending on the target metric, the best outcomes are attained under different interventions� regimes. Our results emphasize the importance of sustained enforcement of Non-Pharmaceutical Interventions on preventing epidemic resurgence due to importation/emergence of novel variants. We also discuss how our methods can be used to study when a novel variant emerges within a population. Copyright © 2023 the Author(s).

Item Type: Journal Article
Publication: Proceedings of the National Academy of Sciences of the United States of America
Publisher: National Academy of Sciences
Additional Information: The copyright for this article belongs to author.
Keywords: genomic DNA, Article; basic reproduction number; biosurveillance; computer model; decomposition; disease surveillance; disease transmission; epidemic; genetic polymorphism; genomics; geographic distribution; hospitalization; human; immune response; immunization; mathematical model; pandemic; prevalence; public health; vaccination; adolescent; article; biosurveillance; coronavirus disease 2019; cross infection; disease surveillance; epidemic, COVID-19; Disease Outbreaks; Genomics; Humans; Pandemics; Public Health
Department/Centre: Division of Electrical Sciences > Electrical Communication Engineering
Division of Interdisciplinary Sciences > Centre for Biosystems Science and Engineering
Division of Interdisciplinary Sciences > Robert Bosch Centre for Cyber Physical Systems
Date Deposited: 01 Mar 2024 05:39
Last Modified: 01 Mar 2024 05:39
URI: https://eprints.iisc.ac.in/id/eprint/83814

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